This might apply to other distros of Linux but after upgrading Linux Mint from 18 to 18.1 my Steam Controller stopped working properly in games. Here are the steps I took to fix it. Firstly unplug the steam controller and/or the wireless device.

After the 18.1 upgrade I found that Mint removed a package named steam-devices, so go ahead and open a terminal to reinstall this.

$ sudo apt install steam-devices

Installing this will rewrite your udev rules so we need to fix that up, but thats ok as of 11/22/16 the udev rules needed to be updated anyway.

Open the udev file for the steam controller, if you're using mint you most likely have xed as a text editor, if you don't just drop in whatever you want; gedit, ect. If using a terminal editor like nano or vim replace gksudo with sudo (gksudo is just for GUI programs).

$ gksudo xed /lib/udev/rules.d/99-steam-controller-perms.rules

Then copy the following and paste it in, replacing any text (if any) that exist in that file.

Update Dec 27th: Thanks to /u/pizza-dude for reminding me to use gksudo with GUI related programs in sudo.Update Jan 24 2017: Changed the group to "games" something most users are already apart of to begin with. Found this bug out when trying to game on my laptop.